Activation of macrophages by inflammatory stimuli induces reprogramming of mitochondrial metabolism to support the production of pro-inflammatory cytokines and nitric oxide. Hallmarks of this metabolic rewiring are downregulation of α-ketoglutarate formation by isocitrate dehydrogenase (IDH) and accumulation of glutamine-derived succinate, which enhances the inflammatory response via the activity of succinate dehydrogenase (SDH). Here, we identify the nuclear receptor Nur77 (Nr4a1) as a key upstream transcriptional regulator of this pro-inflammatory metabolic switch in macrophages. Nur77-deficient macrophages fail to downregulate IDH expression and accumulate higher levels of succinate and other TCA cycle-derived metabolites in response to inflammatory stimulation in a glutamine-independent manner. Consequently, these macrophages produce more nitric oxide and pro-inflammatory cytokines in an SDH-dependent manner. In vivo, bone marrow Nur77 deficiency exacerbates atherosclerosis development and leads to increased circulating succinate levels. In summary, Nur77 induces an anti-inflammatory metabolic state in macrophages that protects against chronic inflammatory diseases such as atherosclerosis.
Pubmed ID: 30134173 RIS Download
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A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor''''s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor''''s activating or repressive function. BETA requires ~2GB RAM and 1h for the whole procedure. BETA may run on the web server at Cistrome or may be downloaded.
View all literature mentionsPortal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
View all literature mentionsSoftware for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
View all literature mentionsSoftware Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.
View all literature mentionsSoftware tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
View all literature mentionsSoftware for a genome wide mapping data interpretation platform for NGS (ChIPSeq).
View all literature mentionsSoftware tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSet of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.
View all literature mentionsAn Antibody supplier and subset of ThermoFisher Scientific which provides fluorescence reagents for various experiments and methods.
View all literature mentionsA software which acquires and processes data sets, primarily through the Xcalibur system.
View all literature mentionsSoftware program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.
View all literature mentionsAllele Detail: Targeted This is a legacy resource.
View all literature mentionsCell line RAW 264.7 is a Cancer cell line with a species of origin Mus musculus
View all literature mentionsCell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)
View all literature mentionsThis monoclonal targets Smooth Muscle Actin
View all literature mentionsThis monoclonal targets Human CD3
View all literature mentionsThis monoclonal targets Mac-3
View all literature mentionsThis monoclonal targets SDHA
View all literature mentionsThis polyclonal targets iNOS antibody
View all literature mentionsThis unknown targets HIF-1 alpha
View all literature mentionsThis monoclonal targets IL-1-beta
View all literature mentionsThis polyclonal targets β-actin
View all literature mentionsThis monoclonal targets Beta-Tubulin antibody Clone dm1a
View all literature mentionsThis monoclonal targets HA tag
View all literature mentionsMus musculus with name B6.129S7-Ldlrtm1Her/J from IMSR.
View all literature mentionsMus musculus with name B6.C-Tg(CMV-cre)1Cgn/J from IMSR.
View all literature mentionsOpen source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
View all literature mentionsStatistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsMus musculus with name B6.129S7-Ldlrtm1Her/J from IMSR.
View all literature mentionsMus musculus with name B6.C-Tg(CMV-cre)1Cgn/J from IMSR.
View all literature mentionsOpen source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
View all literature mentionsStatistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsThis monoclonal targets Smooth Muscle Actin
View all literature mentionsThis monoclonal targets Human CD3
View all literature mentionsThis monoclonal targets Mac-3
View all literature mentionsThis monoclonal targets SDHA
View all literature mentionsThis polyclonal targets iNOS antibody
View all literature mentionsThis unknown targets HIF-1 alpha
View all literature mentionsThis monoclonal targets IL-1-beta
View all literature mentionsThis polyclonal targets β-actin
View all literature mentionsThis monoclonal targets Beta-Tubulin antibody Clone dm1a
View all literature mentionsThis monoclonal targets HA tag
View all literature mentionsMus musculus with name B6.129S7-Ldlrtm1Her/J from IMSR.
View all literature mentionsMus musculus with name B6.C-Tg(CMV-cre)1Cgn/J from IMSR.
View all literature mentionsOpen source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
View all literature mentionsStatistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsThis monoclonal targets Smooth Muscle Actin
View all literature mentionsThis monoclonal targets Human CD3
View all literature mentionsThis monoclonal targets Mac-3
View all literature mentionsThis monoclonal targets SDHA
View all literature mentionsThis polyclonal targets iNOS antibody
View all literature mentionsThis unknown targets HIF-1 alpha
View all literature mentionsThis monoclonal targets IL-1-beta
View all literature mentionsThis polyclonal targets β-actin
View all literature mentionsThis monoclonal targets Beta-Tubulin antibody Clone dm1a
View all literature mentionsThis monoclonal targets HA tag
View all literature mentions